IDENTIFICATION OF EPILEPSY MODIFIER GENES IN A MOUSE MODEL By Nicole Alise Hawkins Dissertation Submitted to the Faculty of the Graduate School of Vanderbilt University in partial fulfillment of the requirements for the degree of DOCTOR OF PHILOSOPHY In Neuroscience December 2013 Nashville, Tennessee Approved: Jennifer Kearney, Ph.D. Alfred George, Ph.D. E. Michelle Southard-Smith, Ph.D. Douglas Mortlock, Ph.D. To my parents, for their endless support and To my husband, who fulfills my life, one giggle at a time ii ACKNOWLEDGEMENTS This work would not have been possible without the financial support of the NIH. Specifically, I would like to acknowledge the Training Program in Ion Channel and Transporter Biology (NINDS/NIH T32- NS007491), the NINDS for the Ruth L. Kirschstein National Research Service Award Predoctoral Fellowship (F31 NS077700- 01) and the RO1 (NINDS NS053792) funding from my mentor, Dr. Jennifer Kearney. Additionally, I am grateful for the Epilepsy Foundation Predoctoral Research Training Fellowship that I was awarded. Furthermore, I would like to thank the Vanderbilt Graduate School and Vanderbilt Kennedy Center for the numerous travel grants I was awarded that allowed for travel to several important conferences. I must first acknowledge my mentor, Dr. Jennifer Kearney. I had an incredible graduate school experience because of her. She developed my skills as a lab scientist, geneticist, writer and mouse colony connoisseur. I quickly learned that mouse and lab research does not always go as planned. However, Dr. Kearney taught me to laugh it off and try again the next day. I will be forever grateful for the time spent in her lab. I hope in the future I can also be the extraordinary scientist, wife and mother that she is today. Thank you. I am grateful to all members of the Kearney lab, past and present. In particular, I would like to acknowledge Sarah Bergren, Rebecca Somershoe and Elizabeth Rutter for generating the chromosome 11 interval specific congenic strains that I maintained throughout the years. I would like to also thank Elizabeth and Vanessa Thompson for guiding me in the basic operations of our lab and mouse work essentials. I am thankful to iii our current lab members Ben Jorge, Jae Maeng, Clint McCollom and Alison Miller who have helped me in countless ways along this journey. I would also like to thank our pseudo lab members, Dr. Chris Thompson and Lyndsey Anderson from the George lab, for all of their contributions to my project, both scientific and not. I am appreciative to each of the members of my dissertation committee, who have all contributed to the success of my project. Thank you to Dr. Al George for being the chair of my committee as well as the co-sponsor on my NINDS NRSA. Additionally, I would like to express gratitude towards Dr. George for involving me in the Ranolazine drug studies, where I was able to learn the fundamentals of pharmacology. I would like to thank Dr. Michelle Southard-Smith for advancing my comprehension of genetics and mouse generation, as well as always keeping me on my toes during exams and committee meetings. I also would like to acknowledge Dr. Doug Mortlock for his persistence on generating our BAC transgenic models. Additionally, I would like to thank him for the use of his lab equipment for BAC preparation. I am also grateful to the Vanderbilt Technologies for Advanced Genomics Core, especially Christian Shaffer, Travis Clark and Chelsea Baker for the assistance and effort on our RNA-Seq experiments. I need to express gratitude toward the Vanderbilt Transgenic Mouse/ES Cell Shared Resource, especially Jennifer Skelton, on their determination to produce our BAC transgenic and knockout mouse lines. I am also very appreciative to the entire Vanderbilt DAC staff for their daily care and maintenance of our mouse facilities. I finally want to express gratitude towards the enormous support network that is my family. My parents have promoted education since the day I was born. It was never iv “If you go to college” it was always “When”. They never discouraged my desire to attend college out of state and were always ready for a road trip to Purdue. While they may not have understood what exactly I was working on in graduate school, they were always willing to read my papers and tell everyone about them. Their unconditional love and support has made me the person I am today. I would like to thank my husband, Travis, for his everlasting support of my academic and professional dreams. Travis had no qualms about where I pursued my graduate studies, even knowing he would have to leave Indiana; He only requested a warmer location! He happily read my papers and listened to my talks. He drove me to campus countless times on the weekends. Travis’ love and support for my science dreams has enabled me to become a successful scientist. Finally, I want to thank my “little” brother Anthony. His battle with epilepsy is my motivation each day to get into the lab. I hope every day that advances will be made to cure this dreadful disease. Thank you for the world, Mom, Dad, Travis and Anthony. v TABLE OF CONTENTS Page DEDICATION .................................................................................................................. ii ACKNOWLEDGEMENTS ............................................................................................. iii LIST OF TABLES ........................................................................................................... ix LIST OF FIGURES ........................................................................................................... x LIST OF ABBREVIATIONS ......................................................................................... xii Chapter I. INTRODUCTION ............................................................................................ 1 Epilepsy ...................................................................................................... 1 Voltage-Gated Sodium Channels ............................................................... 2 Voltage-Gated Sodium Channels and Epilepsy ......................................... 3 Variable Expressivity of Sodium Channel Mutations in Epilepsy ............ 7 Epilepsy Models With Sodium Channel Mutations .................................. 8 Genetic Background Influences Epilepsy Models ................................... 11 Genetic Modifiers of Epilepsy ................................................................. 12 Conclusions and Specific Aims ............................................................... 15 References ................................................................................................ 18 II. CONFIRMATION OF AN EPILEPSY MODIFIER LOCUS ON MOUSE CHROMOSOME 11 AND CANDIDATE GENE ANALYSIS BY RNA-SEQ ............................................................................ 30 Introduction .............................................................................................. 30 Materials and Methods ............................................................................. 32 Mice .................................................................................................. 32 Generation of ISC Lines ................................................................... 32 Genotyping ....................................................................................... 33 Phenotyping ...................................................................................... 33 Statistical Analysis ............................................................................ 34 RNA Isolation ................................................................................... 34 Sample Preparation for RNA-Seq .................................................... 34 RNA-Seq Data Analysis ................................................................... 35 Results ...................................................................................................... 37 Interval-Specific Congenics .............................................................. 37 vi ISC Phenotyping ............................................................................... 38 ISC X B6.Q54 Survival .................................................................... 41 Candidate Gene Analysis by RNA-Seq ............................................ 42 Discussion ................................................................................................ 51 References ................................................................................................ 57 III. VALIDATION OF CACNA1G AND HLF AS GENETIC MODIFIERS OF THE SCN2AQ54 EPILEPSY PHENOTYPE .............................................. 63 Introduction .............................................................................................. 63 Materials and Methods ............................................................................. 66 Mice .................................................................................................. 66 Genotyping ....................................................................................... 67 BAC Integrity, Copy Number and Expression ................................. 68 Generation of Double Mutant Mice .................................................. 69 Phenotyping ...................................................................................... 70 Pyridoxine Deficient and Enriched Diets ......................................... 71 Neurochemistry ...............................................................................